Does Blender support texture with straight alpha
This behaviour seems to be internal, so no easy way to modify it.
But a way to facilitate that duplication process is to instead of duplicating the texture file itself, duplicating the Image datablock that references the file inside Blender.


Create the Image Texture node as usual and duplicate it, and then click the user number to make a new copy of the Image datablock -- they will both reference the same file but have separate Use Alpha settings.